Also these samples from the Ian Logan spreadsheet haven’t these mutations. If you had studied mtDNA (and of Basques above all) you would know that they have many back mutations, also in my haplogroup K, and this demonstrates their ancientness.

Alu I 7025 is a RFLPs test, for example the sample from La Chora, Cantabria, which tested HVR-I 16093-16362, Jean Manco mentioned that it could also be R0a1b instead of the H6 that was reported. The way the authors could be able to differentiate between R0 and H6 would be do a restriction enzyme test, or RFLP analysis. If the sample turns out to be Alu I 7025 +, then it is definitely R0, because H is Alu I 7025-. You can look at Table-3 of this study to see how they can test for haplogroups using RFLPs.

OK I understand. The RFLP markers are small fragments of DNA which comprise one mutation defining one haplogroup.For example Alu I 7025 comprises the mutation 7028 which defines the H haplogroup, Mse I 14766 comprises the mutation 14766 which defines the HV haplogroup, Dde I 10394 comprises the mutation 10398 which defines the J haplogroup, Nla III 4577 comprises the mutation 4580 which defines the V haplogroup, and so on...

Dienekes: In short, I am quite skeptical of this result, and in all probability it will turn out to be either contamination or misplaced archaeological context.

Lohizun: The authors went through great lengths to avoid contamination. It is by far more likely that Behar et al (2012) estimated the age of Haplogroup H erroneously, than this samples are either contaminated or not Magdalenian. You have gotten to the point where you are arguing against empirical evidence based on pre-conceive notions.Saturday, April 28, 2012 12:03:00 AM

Lohizun: You have gotten to the point where you are arguing against empirical evidence based on pre-conceive notions.

Dienekes: Incorrect, I am sceptical of anomalous and incomplete evidence.

Lohizun: It is by far more likely that Behar et al(2012) estimated the age of Haplogroup H erroneously

Dienekes: Your claim that it is "far more likely" is your opinion. Both Behar et al. (2012) and Fu et al. (2012) are consistent with a late origin of mtDNA haplogroup H. This haplogroup was also not detected in many other hunter-gatherer samples from all over Europe and by many different teams of researchers.It is indeed a valuable new piece of evidence, but should be evaluated in the context of the totality of the evidence. If mtDNA haplogroup H was indeed in Europe since Upper Paleolithic times, we will surely find it in other places and by other teams. Until we do, "one swallow doesn't make a summer".Saturday, April 28, 2012 1:06:00 AM

Maju: But it was indeed detected by some other researchers (which you insist in disdaining) precisely in that same region of Europe/North Africa It has also never been detected in your alleged areas of origin (West Asia and such) before Neolithic ever, at least not with any certainty. While I do not think it is the case, it's even possible that H was semi-restricted to parts of SW Europe and NW Africa before Neolithic. Although we still need a source for the H found in Neolithic Central Europe (Austria?)But in any case this is much more solid than "molecular-clock-o-logy". You're grasping for straws. Saturday, April 28, 2012 2:10:00 AM

Gioiello: I find marvellous this exchange of letters between Dienekes and Maju and Lohizun on “Dienekes’ Anthropology blog”. There is here also much of my works in these last years, above all to not fear authorities and who gets massive funds.

When one of the authors of the study Concepcion de la Rua said to Maju on an email:

Quote from: Concepcion de la Rua

We have also performed PCR-RLFPs with the purpose of determining the SNPs from the coding region and therefore confirm the haplogroup to which each of the haplotypes obtained by sequenciation belong. The enzimes we used appear in several bibliographic citations in the article (17, 20, 42, 63).

About the question that you ask on the matter of the determination of haplogroup H, the answer is that we have indeed used the enzyme Alu I to determine the SNP in position 7025 of the coding region of mtDNA.

So the sample from La Pasiega, Cantabria was tested for the SNP in position 7025, therefore it can't be HV, or R0. The same procedure revealed that the sample from La Pasiega, Cantabria couldn’t be U because it tested negative for the respective SNP that defines U.

In any case, even if they hadn’t done the RFLP test there is still a possibility that the haplogroup might have been H. So it makes me wonder why Jean Manco would rather show the sample from La Pasiega as U? Instead of “H6”, does she have any proof that would support that being U instead of H6. Wouldn't it be more correct, to list it as “U or H6” instead.

Again if you two bothered to read the references they provided, instead of jumping on the bandwagon that there isn't enough information, you would have noticed that they did in fact test for RFPLs/restriction enzyme test.

If you bothered to read the entire paper you would know that they did NOT report results for a test that they imply that they did. Obviously you don't need to see the actual data because you like the result they presented. And then you arrogantly criticize people who object that the paper does not include the actual data.

Anyone who is interested in knowledge will admit that there is still uncertainty in these test results, and that we really need coding region results. Those who only want to confirm their prejudice are perfectly happy with the lack of data presented.

In my opinion it is a waste of time and money to continue doing only HVR1 tests on ancient remains. I don't think we can resolve this debate until we see full genome mtDNA for ancient remains.

If you bothered to read the entire paper you would know that they did NOT report results for a test that they imply that they did. Obviously you don't need to see the actual data because you like the result they presented. And then you arrogantly criticize people who object that the paper does not include the actual data.

Actually sir, if you bothered to read the entire paper you would have come across the portion where the authors said the following:

Quote from: Hervella.et.al.2012

In order to classify the mitochondrial variability of the individuals analyzed in this study, we proceeded to amplify 11 markers, which are required for defining the 10 Caucasian haplogroups described [63]. The protocol and primers are described in [17,20,42].

Now, if instead of projecting yourself like you are doing, and throwing nonsensical moronic Ad Hominems, you would have taken the time to read through the references you would have known that the authors performed RFPL analyses.

Anyone who is interested in knowledge will admit that there is still uncertainty in these test results, and that we really need coding region results. Those who only want to confirm their prejudice are perfectly happy with the lack of data presented.

In my opinion it is a waste of time and money to continue doing only HVR1 tests on ancient remains. I don't think we can resolve this debate until we see full genome mtDNA for ancient remains.

Apparently you aren’t interested in knowledge then, because, a person who is truly interested in confirming whether or not they did perfom RFPL analysis would email the authors and ask them about it, if he/she remained skeptical after reading throught the references. Though from the references they provide it is clear enough that the authors used a combo of HVR-I+HVR-II+RFLP analyses. Nonetheless, thankfully the blogger Maju emailed the author of the study, just to confirm that the analyses were indeed done, and the confirmation was received.

The thing is that this study was subject to the same level of deep testing(i.e. HVR-I, HVR-II, and RFPL) that Bramanti et al.2009, and if the results of Bramanti.et.al.2009 are gladly taken by many is conclusive proof that mt-DNA U4 and mt-DNA U5 were present in Magdalenian samples from Central Europe, I think it is rather a double standard to accept one study over the other, when both did the same analyses. The only prejudice shown here, is that of people like you, who without having a clue, are throwing Ad Hominems left and right to try to fit their pre-conceived notions of the world. Whether you like it or not, mt-DNA H and mt-DNA H6 were found in Magdalenian Cantabria, and what’s more, the data is being used in different studies, so there is more to come.

Conclusion: There isn't lack of data, there is positively strong bias which leads to unwilligness to accept data that doesn't fit with pre-conceived notions, leading to the development of logical fallacies such as Ad Hominems, Special Pleadings, amongst other things.

Actually sir, if you bothered to read the entire paper you would have come across the portion where the authors said the following:

I did read the paper and the reference and then I looked for the data in the paper and the supplements. If they did the test, why not present the data? We are supposed to take it on faith. Sorry to be so rude, but reading through the posts above, I'm really irritated by your arrogance in attacking people who simply ask "where is the data?" You should be asking the same question.

But really, the key point is that we need full genome testing. Anything less leaves too much uncertainty in the results.

There are some really awful papers being published on mtDNA in Europe, starting with the postulate that H was present among the earliest Europeans and interpreting the data to prove what they already assumed to be true. Perhaps it will turn out that current age estimates are wrong, and implausible as it seems, H was present in Europe more than 25,000 years ago. But you will need FMS testing of ancient DNA to support that argument.

I did read the paper and the reference and then I looked for the data in the paper and the supplements. If they did the test, why not present the data? We are supposed to take it on faith. Sorry to be so rude, but reading through the posts above, I'm really irritated by your arrogance in attacking people who simply ask "where is the data?" You should be asking the same question.

I did ask myself the same question, and I got an answer once I read through the references, and confirmed it once I saw the reply of two of the main authors to a friend of mine who emailed them. I said the following (on this very same thread, just a few posts before) :

Quote

Alu I 7025 is a RFLPs test, for example the sample from La Chora, Cantabria, which tested HVR-I 16093-16362, Jean Manco mentioned that it could also be R0a1b instead of the H6 that was reported. The way the authors could be able to differentiate between R0 and H6 would be do a restriction enzyme test, or RFLP analysis. If the sample turns out to be Alu I 7025 +, then it is definitely R0, because H is Alu I 7025-. You can look at Table-3 of this study to see how they can test for haplogroups using RFLPs. http://onlinelibrary.wiley.com/doi/10.1046/j.1529-8817.2005.00170.x/pdf

Of course it is far easier for you to attack my argument on the basis that according to you I’m arrogant and that irritates you, which is why I too got irritated, because what does that have to do with anything, starting with the fact that I don’t have to explain these results, and that I have gone out of my way with the references to try to get people to comprehend it, yet all I get is a poorly coded Ad Hominem thrown my way.

But really, the key point is that we need full genome testing. Anything less leaves too much uncertainty in the results.

But the key point here, is that you know very well that full genome sequencing of ancient mt-DNA is something that is completely out of our reach, so by setting the skepticism bar at complete genome sequencing, you are once more leaving room for all speculations to be made once more, because in the meantime, I assure you, people will still take the results from Bramanti et.al.2009(Who didn't do full genome sequencing either BTW) at face value to argue for the presence of mt-DNA U as being the sole pre-Neolithic European lineage based on the presence of mt-DNA U in Magdalenian Central Europe.

What I see, is that you are questioning the scientific integrity of the team of authors that published this paper, based on the fact that you consider them to be less transparent. I agree, they should have shown that when they say that something that is HVR-I CRS, and HVR-II 73G, they should have also shown that it was positive for Hinf-I 12308, indicating that it is a U. However, the authors felt that it was sufficient to reference that to previous studies, and it is ok to reference one's previous studies if one doesn’t want to extend oneself. Now, you are telling me that by simply showing the RFPL results on the supplementary file Bramanti et al.2009 is far more reliable than Hervella.et.al.2012, who actually referenced previous studies for the methodology used to sample RFPL, and who, moreover took the time to confirm to readers in doubt that they did indeed performed both coding region and control region tests? You see, this isn’t one of those things of where I pick the results I like, otherwise I could bring up the results of Chandler.et.al.2005 where only HVR-I was used to determine the presence of mt-DNA H in a Mesolithic Portuguese sample. This is yet one more example of people who have pre-conceived notions acting out on them, and the irony, is that you are projecting yourself.

There are some really awful papers being published on mtDNA in Europe, starting with the postulate that H was present among the earliest Europeans and interpreting the data to prove what they already assumed to be true. Perhaps it will turn out that current age estimates are wrong, and implausible as it seems, H was present in Europe more than 25,000 years ago. But you will need FMS testing of ancient DNA to support that argument.

You mean an Ad Hoc approach, I can find tons and tons of papers that use it, and they are certainly not talking about mt-DNA H. Nonetheless, like I said, those samples from La Chora, and La Pasiegas are being resequenced for usage in other studies, so there is more to come. I won’t really need FMS to support my argument, why would I GST, there would be those (likely the majority/99%) that would accept the scientific breakthroughs of our times, whereas they will be those(likely in the minority/1%) who would remain skeptical no matter what, and will always find a way to try to question the integrity of data that doesn’t fit with their pre-conceived notions. So once more, I can only do one thing, and forgive me for it, but like I said over at Maju’s blog regarding the user Ponto who shares a very close M.O with you:

Quote

Ponto will continue to disbelieve anything that doesn't fit his biased notions of haplogroups. So there really isn't anything(other than ignore him) to be done here.

I did ask myself the same question, and I got an answer once I read through the references, and confirmed it once I saw the reply of two of the main authors to a friend of mine who emailed them. I said the following (on this very same thread, just a few posts before) :

Quote

Alu I 7025 is a RFLPs test, for example the sample from La Chora, Cantabria, which tested HVR-I 16093-16362, Jean Manco mentioned that it could also be R0a1b instead of the H6 that was reported. The way the authors could be able to differentiate between R0 and H6 would be do a restriction enzyme test, or RFLP analysis. If the sample turns out to be Alu I 7025 +, then it is definitely R0, because H is Alu I 7025-. You can look at Table-3 of this study to see how they can test for haplogroups using RFLPs. http://onlinelibrary.wiley.com/doi/10.1046/j.1529-8817.2005.00170.x/pdf

You still don't understand - they say they did a test but they never reported the results. I already know how they can test CR SNPs. I want to see results showing that they actually did test CR SNPs.

The fact that you were attacking people for asking for the CR SNP results was what irritated me. And I still have not seen those test results - I've only heard that they emailed someone to say that they did the test.

But the key point here, is that you know very well that full genome sequencing of ancient mt-DNA is something that is completely out of our reach, so by setting the skepticism bar at complete genome sequencing, you are once more leaving room for all speculations to be made once more, because in the meantime, I assure you, people will still take the results from Bramanti et.al.2009(Who didn't do full genome sequencing either BTW) at face value to argue for the presence of mt-DNA U as being the sole pre-Neolithic European lineage based on the presence of mt-DNA U in Magdalenian Central Europe.

Why is it out of reach? In some cases you can get definitive results from an HVR1 test, for a haplogroup that has several SNPs in a unique combination, but in many cases you cannot get a good ID. I don't think we can rely on any ancient mtDNA identification based on CRS or on a single SNP. Even if they can't sequence the full genome, they should at least test several SNPs needed for confirmation. The new Lacan et al work shows how challenging this is.

You still don't understand - they say they did a test but they never reported the results. I already know how they can test CR SNPs. I want to see results showing that they actually did test CR SNPs. The fact that you were attacking people for asking for the CR SNP results was what irritated me. And I still have not seen those test results - I've only heard that they emailed someone to say that they did the test.

Well, them not including the actual table where it shows that CRS tested for Alu I 7025- is basically why you are questioning the validity of their findings? Because like I said the blogger Maju emailed the authors asking them if they had done the RFLP analyses or not, and he got replies from two of the authors:

Why is it out of reach? In some cases you can get definitive results from an HVR1 test, for a haplogroup that has several SNPs in a unique combination, but in many cases you cannot get a good ID. I don't think we can rely on any ancient mtDNA identification based on CRS or on a single SNP. Even if they can't sequence the full genome, they should at least test several SNPs needed for confirmation. The new Lacan et al work shows how challenging this is.

Well basically because it is ancient DNA!!! Why do you think not a single study out there has done a complete full genome on ancient mt-DNA, because they can’t, the DNA is far to deteriorated to be able to do a FGS. As for the single SNP vs. multiple, well, from what I read they tested several SNPs not just one. Meaning that if something tested Alu I 7025-, it was probably tested too for Mse I 14766- and Dde I 10394 -, so it was not just one SNP but 3. Again refer to Table-3 of this study:

How about the testing of Neanderthal and Denisovan mtDNA? Those samples are much older. They might have been in conditions with good preservations, but hopefully you can find some modern humans samples that also have good preservation. But in any case. the problem of deterioration makes it more important to test the full genome. If you can't accurately test the full genome, then you cannot simply test a small portion and assume those results are accurate.

How about the testing of Neanderthal and Denisovan mtDNA? Those samples are much older. They might have been in conditions with good preservations, but hopefully you can find some modern humans samples that also have good preservation. But in any case. the problem of deterioration makes it more important to test the full genome. If you can't accurately test the full genome, then you cannot simply test a small portion and assume those results are accurate.

Well both the Neanderthal and the Denisovan are different species, so it was in the interest of all to fully sequence their genome to see how long age they diverged from AMH. So if we were to impose the policy of only those aDNA samples that have been fully sequences can be published, then we will be lucky if we get one or two aDNA results in the next 20 years or so. So yeah, you can be as skeptical as you want and claim that the results aren’t accurate, but that is your opinion, and it is not mainstream.

I hope you are overly pessimistic. A large part of the effort and cost is sample preparation and controlling for contamination. After going to all that work it seems a shame to only sequence a very small region of the sample. It would be worth the effort to sequence the full genome.

Well both the Neanderthal and the Denisovan are different species, so it was in the interest of all to fully sequence their genome to see how long age they diverged from AMH. So if we were to impose the policy of only those aDNA samples that have been fully sequences can be published, then we will be lucky if we get one or two aDNA results in the next 20 years or so. So yeah, you can be as skeptical as you want and claim that the results aren’t accurate, but that is your opinion, and it is not mainstream.

A full genome test result was just published for a 7000 year old sample "Genomic Affinities of Two 7,000-Year-Old Iberian Hunter-Gatherers" This is exactly what I hoped to see. The sample is U5b2c1 and is significantly older than the Behar et al age estimate of about 4000 years, although it is within the uncertainty rage of their estimate. It establishes a direct link to U5b2c1 test results in Ireland, the UK and Spain. The HVR1 test result provided little useful detail, so it was very important to do the FMS on this sample. More dicussion at:http://dienekes.blogspot.ca/2012/06/mesolithic-iberians-la-brana-arintero.html